International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, p. 191

Section 3.6.8.2. Citation of software packages

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.8.2. Citation of software packages

| top | pdf |

The categories describing software citations are as follows:

COMPUTING group
 COMPUTING
 SOFTWARE

It is expected that citations of software packages in an mmCIF will be made using data items in the SOFTWARE category. However, in some cases, a particular publisher or database may require that this information is given using data items in the COMPUTING category instead (see Section 3.2.5.2[link] for details).

Data items in these categories are as follows:

(a) COMPUTING [Scheme scheme188]

(b) SOFTWARE [Scheme scheme189]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_).

The data item _computing.entry_id has been added to the COMPUTING category to provide the formal category key required by the DDL2 data model.

The data items in the SOFTWARE category are used to cite the software packages used in the structure analysis. The software can be described in great detail if necessary. However, for most applications a small subset of these data items, for example just _software.name and _software.version, could be used (see Example 3.6.8.1[link]).

Example 3.6.8.1. The refinement program Prolsq described with data items in the SOFTWARE category.

[Scheme scheme190]

Most data items in the SOFTWARE category are self-explanatory, but a few require further comment. The data item _software.citation_id provides a way to link the details of a program to the citation of an article in the literature that describes the program; this data item must match a value of _citation.id in the CITATION category. The name and e-mail address of the author of the software can also be given using _software.contact_author and _software.contact_author_email, respectively. (This may be the original author or someone who subsequently modifies or maintains the software; these data items would generally refer to the person most closely associated with the maintenance of the code at the time it was used.) The release date of the software may be recorded in _software.date. As far as possible, the date should be that of the version recorded in _software.version. The data item _software.location may be used to supply a URL from which the software may be downloaded or where it is described in detail.








































to end of page
to top of page